public void AddAndGetAlleleCounts()
{
var testRegion = new MyRegionState(1000, 2000);
for (var i = 0; i < 5; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.A, DirectionType.Forward);
}
for (var i = 0; i < 2; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.C, DirectionType.Forward);
}
for (var i = 0; i < 12; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.C, DirectionType.Reverse);
}
for (var i = 0; i < 15; i++)
{
testRegion.AddAlleleCount(2000, AlleleType.A, DirectionType.Stitched);
}
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.A, DirectionType.Forward), 5);
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.C, DirectionType.Forward), 2);
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.C, DirectionType.Reverse), 12);
Assert.Equal(testRegion.GetAlleleCount(2000, AlleleType.A, DirectionType.Stitched), 15);
Assert.Equal(testRegion.GetAlleleCount(1000, AlleleType.A, DirectionType.Stitched), 0);
Assert.Equal(testRegion.GetAlleleCount(1500, AlleleType.A, DirectionType.Forward), 0);
}
protected MyRegionState GetBlock(int position, bool addIfMissing = true)
{
if (position <= 0)
{
throw new ArgumentException("Position must be greater than 0.");
}
if (_lastAccessedBlock != null && _lastAccessedBlock.ContainsPosition(position)) // performance improvement to remember last block
{
return(_lastAccessedBlock);
}
var blockKey = GetBlockKey(position);
MyRegionState block;
if (!_regionLookup.TryGetValue(blockKey, out block))
{
if (!addIfMissing)
{
return(null);
}
block = CreateOrReuseBlock((blockKey - 1) * _regionSize + 1, blockKey * _regionSize);
_regionLookup[blockKey] = block;
}
_lastAccessedBlock = block;
return(block);
}
public void AddAndGetCandidates_Errors()
{
var testRegion = new MyRegionState(1000, 2000);
Assert.Throws <ArgumentException>(
() => testRegion.AddCandidate(new CandidateAllele("chr1", 999, "A", "T", AlleleCategory.Snv)));
Assert.Throws <ArgumentException>(
() => testRegion.GetAlleleCount(2001, AlleleType.A, DirectionType.Forward));
}
private List <int> GetAllRefCounts(MyRegionState testRegion)
{
var refCounts = new List <int>();
for (int position = testRegion.StartPosition; position <= testRegion.EndPosition; position++)
{
refCounts.Add(testRegion.GetGappedMnvRefCount(position));
}
return(refCounts);
}
/// <summary>
/// Get block by either reusable one that is available for reuse, or creating a new one if non available for reuse.
/// </summary>
/// <param name="startPosition"></param>
/// <param name="endPosition"></param>
/// <returns></returns>
private MyRegionState CreateOrReuseBlock(int startPosition, int endPosition)
{
MyRegionState block;
if (_reusableBlocks.Any())
{
block = _reusableBlocks.Pop();
block.Reset(startPosition, endPosition);
}
else
{
block = new MyRegionState(startPosition, endPosition);
}
return(block);
}
public void Equality()
{
// happy path
var testRegion = new MyRegionState(1500, 7002);
var otherRegion = new MyRegionState(1500, 7002);
Assert.True(testRegion.Equals(otherRegion));
Assert.True(otherRegion.Equals(testRegion));
// error conditions
otherRegion = new MyRegionState(1501, 7002); // diff start
Assert.False(testRegion.Equals(otherRegion));
otherRegion = new MyRegionState(1500, 7001); // diff end
Assert.False(testRegion.Equals(otherRegion));
Assert.False(testRegion.Equals("otherobject"));
}
public virtual void DoneProcessing(ICandidateBatch batch)
{
var candidateBatch = batch as CandidateBatch;
if (candidateBatch != null)
{
foreach (var key in candidateBatch.BlockKeys)
{
var blockToRemove = _regionLookup[key];
_reusableBlocks.Push(blockToRemove); // save for reuse later
_regionLookup.Remove(key);
if (_lastAccessedBlock != null && _lastAccessedBlock.Equals(blockToRemove))
{
_lastAccessedBlock = null;
}
}
}
}
public void AddAndGetGappedMnvReferenceCounts_Errors()
{
var testRegion = new MyRegionState(50, 150);
testRegion.AddGappedMnvRefCount(150, 10);
var refCountsBefore = GetAllRefCounts(testRegion);
// -----------------------------------------------
// adding at an invalid position should do nothing
// -----------------------------------------------
testRegion.AddGappedMnvRefCount(151, 1);
var refCountsAfter = GetAllRefCounts(testRegion);
Assert.True(refCountsAfter.SequenceEqual(refCountsBefore));
// -----------------------------------------------
// getting at an invalid position should throw exception
// -----------------------------------------------
Assert.Throws <ArgumentException>(() => testRegion.GetGappedMnvRefCount(151));
}
public void AddAndGetGappedMnvReferenceCounts()
{
var testRegion = new MyRegionState(50, 150);
// -----------------------------------------------
// happy path - add a couple of counts,
// getting them should return the same
// -----------------------------------------------
testRegion.AddGappedMnvRefCount(75, 1);
testRegion.AddGappedMnvRefCount(76, 10);
Assert.Equal(1, testRegion.GetGappedMnvRefCount(75));
Assert.Equal(10, testRegion.GetGappedMnvRefCount(76));
// -----------------------------------------------
// happy path - add a couple of counts to existing ref,
// it should be incremented but others should be unchanged
// -----------------------------------------------
testRegion.AddGappedMnvRefCount(76, 3);
Assert.Equal(1, testRegion.GetGappedMnvRefCount(75));
Assert.Equal(13, testRegion.GetGappedMnvRefCount(76));
}
public void ExecuteTest_GetCandidates(bool withReference, bool withIntervals)
{
var testRegion = new MyRegionState(1, 50);
var chrReference = new ChrReference()
{
Name = "chr1",
Sequence = string.Concat(Enumerable.Repeat("A", 50))
};
var snv1 = new CandidateAllele("chr1", 5, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new [] { 10, 5, 0 }
};
var snv2 = new CandidateAllele("chr1", 15, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 5, 0 }
};
testRegion.AddCandidate(snv1);
testRegion.AddCandidate(snv2);
for (var i = 0; i < 5; i++)
{
testRegion.AddAlleleCount(5, AlleleType.A, DirectionType.Stitched); // ref @ variant position
testRegion.AddAlleleCount(6, AlleleType.A, DirectionType.Stitched); // ref by itself
testRegion.AddAlleleCount(10, AlleleType.C, DirectionType.Stitched); // nonref by itself (no ref)
testRegion.AddAlleleCount(15, AlleleType.A, DirectionType.Reverse); // ref (multiple directions) + nonref
testRegion.AddAlleleCount(15, AlleleType.A, DirectionType.Forward);
testRegion.AddAlleleCount(15, AlleleType.T, DirectionType.Reverse);
}
ChrIntervalSet intervals = null;
if (withIntervals)
{
intervals = new ChrIntervalSet(new List <Region>()
{
new Region(3, 6),
new Region(16, 16)
}, "chr1");
}
var expectedList = new List <CandidateAllele>();
expectedList.Add(snv1);
expectedList.Add(snv2);
if (withReference)
{
expectedList.Add(new CandidateAllele("chr1", 5, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 5 }
});
expectedList.Add(new CandidateAllele("chr1", 6, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 5 }
});
expectedList.Add(new CandidateAllele("chr1", 10, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 15, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 5, 5, 0 }
});
}
if (withIntervals)
{
expectedList = expectedList.Where(c => c.Coordinate == 5 || c.Coordinate == 6 || c.Type != AlleleCategory.Reference).ToList();
if (withReference)
{
expectedList.Add(new CandidateAllele("chr1", 3, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 4, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 16, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
}
}
var allCandidates = testRegion.GetAllCandidates(withReference, chrReference, intervals);
VerifyCandidates(expectedList, allCandidates);
}
public void AddAndGetCandidates()
{
// -----------------------------------------------
// simple test case adding candidate to empty region
// -----------------------------------------------
var testRegion = new MyRegionState(1000, 2000);
var snv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 0, 0 }
};
testRegion.AddCandidate(snv1);
var allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 1);
var fetchedCandidate = allCandidates[0];
Assert.True(fetchedCandidate.Equals(snv1));
// -----------------------------------------------
// add same type of candidate but at different position
// -----------------------------------------------
var snv2 = new CandidateAllele("chr1", 1501, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(snv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 2);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add a different type of candidate at same position
// -----------------------------------------------
var deletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 15, 0, 0 }
};
testRegion.AddCandidate(deletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
// -----------------------------------------------
// add same variant, but more coverage
// -----------------------------------------------
var moreSnv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 2, 0, 0 }, ReadCollapsedCounts = new [] { 9, 8, 7, 6 }
};
testRegion.AddCandidate(moreSnv1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented, read counts incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == moreSnv1.ReadCollapsedCounts[i]);
}
// make sure coverage is preserved, read counts preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == 0);
}
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == 0);
}
var moreDeletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 0, 18, 0 }
};
testRegion.AddCandidate(moreDeletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 33);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add insertion that goes off block
// -----------------------------------------------
var edgeInsertion = new CandidateAllele("chr1", 2000, "A", "TCG", AlleleCategory.Insertion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeInsertion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 4);
Assert.Equal(2001, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add mnv that goes off block
// -----------------------------------------------
var edgeMnv = new CandidateAllele("chr1", 1999, "ATCC", "TCGG", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 5);
Assert.Equal(2002, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add deletion that goes off block
// -----------------------------------------------
var edgeDeletion = new CandidateAllele("chr1", 1999, "A" + new string('T', 25), "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeDeletion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 6);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add variant that goes off block but not as far as the deletion did - max endpoint should stay the same
// -----------------------------------------------
var edgeMnv2 = new CandidateAllele("chr1", 1999, "ATCGA", "TCGCT", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 7);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
}
